I find that if you want to poke holes in something you can do it with anything.
This is incorrect.
About the rest of your post - fair enough.
Even the best of Trek you can poke holes in, so I do not see that as incorrect. And almost every story you can do that. Isn't that what red letter media is all about? Or "How it should have ended"?
How you approach a story will have a lot to do with whether you like it or not. I approach them positively and then let the story itself speak to me, sometimes it works and sometimes I still don't like it. Case in point: I wanted to like Prometheus, but in the end hated it; not because I wanted too but because I just thought the story sucked.